2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.analysis;
23 import jalview.datamodel.Alignment;
24 import jalview.datamodel.AlignmentI;
25 import jalview.datamodel.Sequence;
26 import jalview.datamodel.SequenceFeature;
27 import jalview.datamodel.SequenceI;
28 import jalview.gui.JvOptionPane;
30 import static org.hamcrest.MatcherAssert.assertThat;
31 import static org.hamcrest.Matchers.equalTo;
33 import java.util.BitSet;
34 import java.util.Hashtable;
37 import org.testng.Assert;
38 import org.testng.annotations.BeforeClass;
39 import org.testng.annotations.DataProvider;
40 import org.testng.annotations.Test;
46 public class SeqsetUtilsTest
49 @BeforeClass(alwaysRun = true)
50 public void setUpJvOptionPane()
52 JvOptionPane.setInteractiveMode(false);
53 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
57 * test for JAL-2046 bug - duplication of sequence features on reconstructed
60 @Test(groups = { "Functional" })
61 public void testSeqFeatureAddition()
63 SequenceI[] sqset = new SequenceI[] { new Sequence("Aseq1", "AREALSEQ"),
64 new Sequence("Aseq2", "AREALSEQ") };
66 AlignmentI al = new Alignment(sqset);
68 AlignmentI ds = al.getDataset();
69 SequenceFeature sf1 = new SequenceFeature("f1", "foo", 2, 3, "far");
70 SequenceFeature sf2 = new SequenceFeature("f2", "foo", 2, 3, "far");
71 ds.getSequenceAt(0).addSequenceFeature(sf1);
72 Map<String, SeqsetUtils.SequenceInfo> unq = SeqsetUtils.uniquify(sqset, true);
73 SequenceI[] sqset2 = new SequenceI[] {
74 new Sequence(sqset[0].getName(), sqset[0].getSequenceAsString()),
75 new Sequence(sqset[1].getName(), sqset[1].getSequenceAsString()) };
76 Assert.assertSame(sqset[0].getSequenceFeatures().get(0), sf1);
77 Assert.assertTrue(sqset2[0].getSequenceFeatures().isEmpty());
78 ds.getSequenceAt(0).addSequenceFeature(sf2);
79 Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
80 SeqsetUtils.deuniquify(unq, sqset2);
81 // explicitly test that original sequence features still exist because they
82 // are on the shared dataset sequence
83 Assert.assertEquals(sqset[0].getSequenceFeatures().size(), 2);
84 Assert.assertEquals(sqset2[0].getSequenceFeatures().size(), 2);
85 Assert.assertSame(sqset[0].getSequenceFeatures().get(0),
86 sqset2[0].getSequenceFeatures().get(0));
87 Assert.assertSame(sqset[0].getSequenceFeatures().get(1),
88 sqset2[0].getSequenceFeatures().get(1));
92 public Object[][] sequenceAndMask()
94 return new Object[][] {
95 { "AAAABBBBCCCCDDDD", 0xFFFFL, "AAAABBBBCCCCDDDD" },
96 { "AAAABBBBCCCCDDDD", 0x000FL, "AAAA" },
97 { "---A---B---C---D", 0x8888L, "ABCD" },
98 { "---A---B---C---D", 0x9999L, "-A-B-C-D" },
99 { "ABCDABCDABCDABCD", 0xC5A3L, "ABBDACCD" },
101 { "AAAABBBBCCCCDDDD", 0x0000L, "" },
102 { "AAABBBCCC", 0xFFFF, "AAABBBCCC" },
103 { "AAAABBBB", 0xD000L, "" },
104 { "AAAABBBB", 0xAA0AL, "AA" },
108 @Test(groups = {"Functional"}, dataProvider = "sequenceAndMask")
109 public void testFilterSequence(String sequence, long mask, String expected)
111 BitSet bitMask = BitSet.valueOf(new long[] {mask});
112 var result = SeqsetUtils.filterSequence(sequence.toCharArray(), bitMask);
113 assertThat(result, equalTo(expected.toCharArray()));